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Bromine in PDB 1z5m: Crystal Structure of N1-[3-[[5-Bromo-2-[[3-[(1-Pyrrolidinylcarbonyl) Amino]Phenyl]Amino]-4-Pyrimidinyl]Amino]Propyl]-2,2- Dimethylpropanediamide Complexed with Human PDK1

Enzymatic activity of Crystal Structure of N1-[3-[[5-Bromo-2-[[3-[(1-Pyrrolidinylcarbonyl) Amino]Phenyl]Amino]-4-Pyrimidinyl]Amino]Propyl]-2,2- Dimethylpropanediamide Complexed with Human PDK1

All present enzymatic activity of Crystal Structure of N1-[3-[[5-Bromo-2-[[3-[(1-Pyrrolidinylcarbonyl) Amino]Phenyl]Amino]-4-Pyrimidinyl]Amino]Propyl]-2,2- Dimethylpropanediamide Complexed with Human PDK1:
2.7.1.37;

Protein crystallography data

The structure of Crystal Structure of N1-[3-[[5-Bromo-2-[[3-[(1-Pyrrolidinylcarbonyl) Amino]Phenyl]Amino]-4-Pyrimidinyl]Amino]Propyl]-2,2- Dimethylpropanediamide Complexed with Human PDK1, PDB code: 1z5m was solved by M.Whitlow, M.Adler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.17
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 124.610, 124.610, 46.970, 90.00, 90.00, 120.00
R / Rfree (%) 21.2 / 26.9

Other elements in 1z5m:

The structure of Crystal Structure of N1-[3-[[5-Bromo-2-[[3-[(1-Pyrrolidinylcarbonyl) Amino]Phenyl]Amino]-4-Pyrimidinyl]Amino]Propyl]-2,2- Dimethylpropanediamide Complexed with Human PDK1 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Bromine Binding Sites:

The binding sites of Bromine atom in the Crystal Structure of N1-[3-[[5-Bromo-2-[[3-[(1-Pyrrolidinylcarbonyl) Amino]Phenyl]Amino]-4-Pyrimidinyl]Amino]Propyl]-2,2- Dimethylpropanediamide Complexed with Human PDK1 (pdb code 1z5m). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total only one binding site of Bromine was determined in the Crystal Structure of N1-[3-[[5-Bromo-2-[[3-[(1-Pyrrolidinylcarbonyl) Amino]Phenyl]Amino]-4-Pyrimidinyl]Amino]Propyl]-2,2- Dimethylpropanediamide Complexed with Human PDK1, PDB code: 1z5m:

Bromine binding site 1 out of 1 in 1z5m

Go back to Bromine Binding Sites List in 1z5m
Bromine binding site 1 out of 1 in the Crystal Structure of N1-[3-[[5-Bromo-2-[[3-[(1-Pyrrolidinylcarbonyl) Amino]Phenyl]Amino]-4-Pyrimidinyl]Amino]Propyl]-2,2- Dimethylpropanediamide Complexed with Human PDK1


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of N1-[3-[[5-Bromo-2-[[3-[(1-Pyrrolidinylcarbonyl) Amino]Phenyl]Amino]-4-Pyrimidinyl]Amino]Propyl]-2,2- Dimethylpropanediamide Complexed with Human PDK1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br501

b:75.6
occ:1.00
 BR7 A:LI8501 0.0 75.6 1.0
C1 A:LI8501 1.9 39.3 1.0
C6 A:LI8501 2.8 34.3 1.0
C2 A:LI8501 2.9 32.7 1.0
N25 A:LI8501 3.2 25.2 1.0
CD1 A:LEU159 3.2 10.6 1.0
CL A:CL698 3.4 26.1 1.0
CB A:LEU159 3.9 13.0 1.0
CG1 A:VAL96 3.9 3.6 1.0
CB A:ALA109 4.1 11.8 1.0
N5 A:LI8501 4.1 22.7 1.0
CG1 A:VAL143 4.1 11.3 1.0
O A:SER160 4.1 20.9 1.0
N3 A:LI8501 4.2 27.6 1.0
CG A:LEU159 4.2 13.4 1.0
OG1 A:THR222 4.2 13.0 1.0
CG2 A:VAL96 4.5 3.7 1.0
C4 A:LI8501 4.6 26.7 1.0
O A:ALA109 4.6 15.4 1.0
C27 A:LI8501 4.7 18.4 1.0
CB A:THR222 4.8 14.8 1.0
CD1 A:LEU212 4.8 13.2 1.0
CG2 A:VAL143 4.8 8.4 1.0
CG2 A:THR222 4.8 12.5 1.0
CB A:VAL96 4.8 9.6 1.0
CB A:VAL143 4.9 5.8 1.0

Reference:

R.I.Feldman, J.M.Wu, M.A.Polokoff, M.J.Kochanny, H.Dinter, D.Zhu, S.L.Biroc, B.Alicke, J.Bryant, S.Yuan, B.O.Buckman, D.Lentz, M.Ferrer, M.Whitlow, M.Adler, S.Finster, Z.Chang, D.O.Arnaiz. Novel Small Molecule Inhibitors of 3-Phosphoinositide-Dependent Kinase-1. J.Biol.Chem. V. 280 19867 2005.
ISSN: ISSN 0021-9258
PubMed: 15772071
DOI: 10.1074/JBC.M501367200
Page generated: Mon Jul 7 04:00:02 2025

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